VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 02 2021 - 11:33:56 CDT

Hi,
  Given that you're running the older 32-bit VMD, I suspect Axel is
exactly right. I would suggest that you consider installing the new
64-bit VMD 1.9.4 test build and see if that cures your problem.

Best,
  John

On Thu, Sep 02, 2021 at 12:06:30PM -0400, Axel Kohlmeyer wrote:
> The free 7GB do not matter since you are using 32-bit executables and they
> are limited in how much memory they can address.
> On Thu, Sep 2, 2021 at 12:03 PM Jason Hlozek <[1]jason.hlozek_at_live.co.za>
> wrote:
>
> Hi John
> The conventional Snapshot OpenGL render does produce the correct
> '.bmp'.Â
> Re system resources for Tachyon, the GPU is not engaged at all and RAM
> usage increases by 2GBs but there's still 7GBs of free head room by the
> time Tachyon aborts.Â
> The external '.dat' scene file is 422MBs and seems to consist
> predominantly of 3D coordinates so it seems like the grid you reference
> is at least partially built?
> Kind regards
> Jason
>
> --------------------------------------------------------------------------
>
> From: John Stone <[2]johns_at_ks.uiuc.edu>
> Sent: Thursday, 02 September 2021 15:43
> To: Jason Hlozek <[3]jason.hlozek_at_live.co.za>
> Cc: [4]vmd-l_at_ks.uiuc.edu <[5]vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Tachyon not rendering large scenes
> Â
> Have you checked to ensure that you're not running your system out of
> memory? Do you have a conventional OpenGL rendering of the scene in
> question for comparison? When you render the scene to an external
> file,
> how large is the scene file? I notice that in the output you included
> below, there's no console output indicating that spatial acceleration
> grid
> structures were built, despite the fact that you have the +V flag
> enabled.
> That is one of the reasons I'm wondering about the memory exhaustion
> issue. Another possibility is a runaway grid build of some sort, but
> I haven't seen a problem like that for a very long time, so the odds
> are somewhat against it.
>
> Best,
> Â John Stone
> Â [6]vmd_at_ks.uiuc.edu
>
> On Thu, Sep 02, 2021 at 12:29:11PM +0000, Jason Hlozek wrote:
> >Â Â Â Hi
> >Â Â Â I'm trying to render an overlaid view of multiple ligands in the
> same
> >Â Â Â protein pocket (i.e. a very busy scene).
> >Â Â Â If I go above 2-3 protein/ligand pairs in the scene, then VMD
> still writes
> >Â Â Â the scene file and calls Tachyon as usual but after a few
> seconds of
> >Â Â Â processing, instead of proceeding to the completion % bar,
> Tachyon instead
> >Â Â Â just ends with VMD saying the render is complete even though it
> didn't
> >Â Â Â run. The same thing happens if I try to call tachyon from the
> command
> >Â Â Â line:
> >Â Â Â "C:\Program Files (x86)\University of Illinois\VMD>
> .\tachyon_WIN32.exe +V
> >Â Â Â "C:\Users\user-pc\AppData\Local\VirtualStore\Program Files
> >Â Â Â (x86)\University of Illinois\VMD\mmpl3_overlay_test"
> >   Tachyon Parallel/Multiprocessor Ray Tracer  Version 0.99.1
> >   Copyright 1994-2014,   John E. Stone
> <[7]john.stone_at_gmail.com>
> >Â Â Â ------------------------------------------------------------
> >Â Â Â C:\Program Files (x86)\University of Illinois\VMD>"
> >Â Â Â I thought it might be timing out and tried increasing the
> windows Timeout
> >Â Â Â Detection and Recovery (TDR) registry variables as well as
> disabling them
> >Â Â Â but it made no difference.
> >Â Â Â Any suggestions please?
> >Â Â Â Kind regards
> >Â Â Â Jason
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [8]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Â Â Â Â Phone:
> 217-244-3349
> [9]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â
>
> --
> Dr. Axel Kohlmeyer  [10]akohlmey_at_gmail.com  [11]http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> References
>
> Visible links
> 1. mailto:jason.hlozek_at_live.co.za
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:jason.hlozek_at_live.co.za
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:vmd-l_at_ks.uiuc.edu
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. mailto:john.stone_at_gmail.com
> 8. http://www.ks.uiuc.edu/~johns/
> 9. http://www.ks.uiuc.edu/Research/vmd/
> 10. mailto:akohlmey_at_gmail.com
> 11. https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!rj4UDi-KzG2GSD5hO09MyAxrj5BSDVzxkpJZHIwlgXP4XNJHGakyU-WSF9s_cVoelQ$ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/